During his college years Hannigan also played with the Ocean City Barons in the USL Premier Development League. During the 2004 season, he played in 10 games, splitting time with Ryan Carr, and helping the club achieve a rare undefeated season. Hannigan was 7-0-3 as a starter earning five shutouts and remains the club's single-season record holder for goals against average (0.56) and saves (75). He also set the club record for saves in a game when he made 18 stops in a 3-1 win against the Reading Rage on July 17, 2004.

He returned to the United States in 2006 to play for the Rochester Raging Rhinos in 2006, but never saw any first-team action, and moved on to Miami FC in 2007. He was Miami's first-choice goalkeeper throughout the 2007, playing 22 games for the team.

After a year playing indoor soccer with the New Jersey Ironmen in 2008, Hannigan returned to Miami in April, 2009, and played 23 games for the team in the USL First Division before being released at the end of the season.